I am clear about the second part where we run the costing process to generate the accounting entries and transfer it to GL from Payroll.

As for the first part, I was under the impression that each employee will be defined as a supplier in AP and the payments can be made to the employees via AP when this is not possible through payroll (as in global legislation). Is it enough that we define the banks as suppliers?

I am not clear about the customization part. It would be great if you can provide more details on the customization. May be a copy of the MD 50 would help.